Just like John isn't the typical hero protagonist, Felix Hoenikker isn't your typical villainous antagonist. Sure, the guy helps create a weapon of mass destruction and inadvertently murders hundreds of thousands of people. That's a given. But it's not like he's sitting on his moon base, petting a cat, and laughing manically about his grand scheme. He's just your average bloke.
What makes Dr. Hoenikker the antagonist of the story is his outlook on life. His search for truth is selfish, undeterred by what might happen should he discover something horrific like—oh, we don't know—the atomic bomb. And this inability to understand how he harms those around him makes him our antagonist.